nextflow.config

manifest {
  name = 'FLUFLO'
  author = 'Jessica M Caleta'
  homePage = 'https://github.com/j3551ca/fluflo'
  description = 'Phylogenetics in Nextflow'
  mainScript = 'main.nf'
  version = '0.4.0'
}

//pipeline parameters

params {

  //help message
  help = null

  //version number
  version = null

  //conda env local cache
  conda_cache = null 

  //directory containing config/ & data/ folders
  work_dir = "/path/to/data/"

  //reference for alignment
  ref = "${params.work_dir}/config/Ref.gb"

  //reference annotation 
  ref_anno = "NO_FILE"

  //use a specific root for the tree
  root_name = false

  //number of ultrafast bootstraps iq-tree (a command related to iterations;
  // ex. -n 10 for FAST mode, -b 1000 for nonparametric bootstrap, -B 1000 for Ultrafast bs)
  // you can also sneak other iq-tree commands in here like --keep-ident, etc.
  bootstrap = "-n 10"

  //nucleotide substitution model to use during IQ-TREE build
  sub_model = "GTR+I+R"

  //input sequences
  seqs = "${params.work_dir}/data/sequences.fasta"

  //metadata of input sequences
  meta = "${params.work_dir}/data/metadata.csv"

  //strains that are excluded
  drop_strains = "${params.work_dir}/config/dropped_strains.txt"

  //colors used in final auspice visualization
  colors = "${params.work_dir}/config/colors.csv"

  //latitude and longitudes
  lat_long = "${params.work_dir}/config/lat_longs.csv"

  //details for auspice visualization
  auspice = "${params.work_dir}/config/auspice_config.json"

  //refining phylogeny
  divergence_units = "mutations"

  //env variable AUGUR_RECURSION_LIMIT
  recursion_limit = 10000

}

//seamlessly run pipeline on different execution systems by modifying
//the process section of the config file. ex. AWS, SLURM, sun grid engine:

process {
  withName: align {
      cpus = 28
    }
  withName: tree {
      cpus = 28
  }
//  penv='smp'
//  executor='sge'
//  memory='30 GB'
}


profiles {
    conda {
      process.conda = "${projectDir}/environments/ENV.yml"
      conda.createTimeout = '1 h'
      if (params.conda_cache) {
         conda.cacheDir = params.conda_cache
       }
     }

    low_mem {
        process {
            memory = '8 GB'
        }
    }

    medium_mem {
        process {
            memory = '16 GB'
        }
    }

    high_mem {
        process {
            memory = '64 GB'
        }
    }
  }

//html displaying breakdown of time taken to execute workflow
timeline {
  enabled = true
  file = "${params.work_dir}/reports/fluflo_timeline.html"
}

//html of cpu/mem usage
report {
  enabled = true
  file = "${params.work_dir}/reports/fluflo_usage.html"
}

//dag of beast-flow workflow
dag {
    enabled = true
    file = "${params.work_dir}/reports/fluflo_dag.html"
}